Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Gonad
Cell type
KURAMOCHI
Primary Tissue
Ovary
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
Ovarian cancer cell line
cell type
Ovarian cancer cell line
cell line
Kuramochi
chip antibody
CTCF
antibody catalog
61311
antibody lot
N/A
young_id
N/A

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
CTCF ChIP-Seq was performed as previously described (Schmidt et al., Methods, 2009) using 25 μg chromatin and 5 μg anti-CTCF antibody (Active Motif, catalogue number 61311) and chromatin sheared to 100-300 bp fragments using a Covaris E220 evolution Focused Ultrasonicator. ChIP libraries were constructed using the Kapa Hyper Library Preparation kit, quantified and sequenced on an Illumina NextSeq 500 sequencer. Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
37235394
Reads aligned (%)
94.5
Duplicates removed (%)
9.0
Number of peaks
34149 (qval < 1E-05)

hg19

Number of total reads
37235394
Reads aligned (%)
93.8
Duplicates removed (%)
10.5
Number of peaks
34373 (qval < 1E-05)

Base call quality data from DBCLS SRA